Creating nothing but a theory (3)

By: James V. Kohl | Published on: March 30, 2015

Life is physics and chemistry and communication

Any model of biologically-based cause and effect must link atoms to ecosystems via the levels of organization in the diagram. That fact has been known to me since the early 1990s, when I was told that my model must start with sensory input linked to gene activation based on articles like this:

Understanding the bases of sex differences

Excerpt: “The articles in this issue summarize the factors surrounding sex differences with respect to ontogeny, phenotype, and hormone-sensitive actions. They follow a sequence that begins with genetic sex differences and carries through to cell, tissue, organ and, finally, systemic effects of gender.”
My comment: Light-induced amino acid substitutions link cell type differences in plants and animals via the physiology of reproduction, which enables fixation of the amino acid substitutions in populations of organisms that exemplify how ecological variation is linked to nutrient-dependent pheromone-controlled physiology of behavior in species from microbes to man.

Can genetic information be controlled by light?

Excerpt (from 2008): “DNA achieves its high degree of photostability through its complex double-helix structure. The interactions between bases that are stacked one above another within a DNA strand, and the hydrogen bonds between the base pairs of the two complementary single strands in the double-helix play key roles.

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Excerpt (from 2014): “The presence of charged radicals in DNA strands after light absorption may cause reactions—oxidative or reductive damage—currently not considered in DNA photochemistry.”

How genes are permanently silenced by small RNAs

Excerpt (from 2015): “In our experiments, we showed that gene silencing is also maintained in the next generation, even when the original RNA molecule is no longer present. So what we’ve discovered is a wholly epigenetic mechanism: we can alter gene expression across generations – and thus influence cell development – without directly changing the DNA sequence.”

From Fertilization to Adult Sexual Behavior

Excerpt (from 1996): “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes” (see for references p. 337).

Seeing the (UV) light: Previously undetected difference in human mutation rate unique to Europeans

Excerpt (from 2015): “In most organisms, C nucleotides located next to G nucleotides have higher mutation rates than most sites in the genome, and this difference in mutability looks like it might be more extreme within chimp genomes than within human genomes. This is an example of a scenario where one mutation type – in this case, CG->TG – might have increased in rate along the chimp lineage relative to the rates of other mutation types.”
My comment: The ongoing misrepresentations of biologically-based cause and effect that link light-induced amino acid substitutions to cell type differentiation in all genera have become ever more ridiculous. The misrepresentations continue to be placed into the context of ridiculous evolutionary theory more than 40 years years after Dobzhansky wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).
How much longer are serious scientists going to ignore or hide from the fact that the balance of microRNAs to nutrient-dependent microRNAs is altered by the sun’s biological energy and its epigenetic effects on nutrients and their metabolism, which links metabolic networks and genetic networks to the physiology of reproduction via RNA-directed DNA methylation and RNA-mediated amino acid substitutions in all genera?
Clearly, it is not the difference in mutation rates that links ecological variation to ecological adaptations. It is nutrient-dependent RNA-mediated amino acid substitutions and DNA repair linked to the physiology of reproduction. The physiology of reproduction is nutrient-dependent and pheromone-controlled in species from yeasts to primates. We reported the conserved molecular mechanisms of sex differences in cell types, which have since been linked to all cell type differentiation in all cells of all individuals of all species.

Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins

Excerpt: The switch between forms is ascribed to the insertion of a single amino acid in the open-form proteins. Thus, PBP quaternary structure controls excitonic coupling and the mechanism of light harvesting. Comparing organisms with these two distinct proteins will reveal the role of quantum coherence in photosynthesis. 
My comment: Isn’t it time to link what is known about ecological variation and amino acid substitutions from atoms to ecosystems and to dispense with the pseudoscientific nonsense about mutations and evolution? Organisms ecologically adapt or die. Species don’t mutate and become other species.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

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I was drawn here by your query as to why nobody visits your blog (in the blog on Nick Lane’s new book)
The answer, of course, lies mostly in the numbers and access to marketing. Many others have similar problems. You are not alone!
I like what I see here and shall return.
You might like to check out the broader perspective in my recent book “The Intricacy Generator: Pushing Chemistry and Geometry Uphill”. Now available as 336 page illustrated paperback from Amazon, etc.

[…] See first: Creating nothing but a theory (3) […]


A recent claim that tardigrades got a sixth of their DNA from microbes is starting to unravel.
If theorists successfully kill the story about horizontal gene transfer in tardigrades, they will help to delay the end of neo-Darwinism and continue to limit acceptance of Greg Bear’s claims about viruses. Fortunately, Greg Bear included claims that link the control of the viruses to ecological adaptations in tardigrades and all other living genera.
The nutrient-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation via what is known about supercoiled DNA in all species, Greg Bear’s claims now link atoms to ecosystems and his claims can be compared to the pseudoscientific nonsense of the rival’s claims that there is only evidence for contamination in the organized genomes of the tardigrades.
However, if the evidence is viewed in the context of ingested DNA that links fixation of beneficial RNA-mediated amino acid substitutions to protection from virus-driven genomic entropy, all evolutionists will continue to look like biologically uninformed science idiots.

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